def create_species_sbml(metabolites, outputfile):
"""Create a SBML files with a list of species containing metabolites of the input set
Args:
metabolites (set): set of metabolites
outputfile (str): SBML file to be written
"""
document = libsbml.SBMLDocument(2, 1)
model = document.createModel("metabolites")
for compound in metabolites:
compound = compound.strip('"')
name, stype, comp = convert_from_coded_id(compound)
s = model.createSpecies()
sbmlGenerator.check(s, 'create species')
sbmlGenerator.check(s.setId(compound), 'set species id')
# Add name and compartment if found by padmet
if name is not None:
sbmlGenerator.check(s.setName(name), 'set species name')
elif name is None:
logger.warning("No name for " + compound)
if comp is not None:
sbmlGenerator.check(s.setCompartment(comp),
'set species compartment')
elif comp is None:
logger.warning("No compartment for " + compound)
libsbml.writeSBMLToFile(document, outputfile)
def setBounds(self, bounds_path, model_path):
reader = libsbml.SBMLReader()
document = reader.readSBML(model_path)
model = document.getModel()
f = open(bounds_path)
for s in f:
name, idreaction, model_name, lb, ub = s.strip().split("\t")
name = name.replace("-", "")
reaction = model.getReaction(name)
if reaction is None:
# test if there is a reaction starting with a
# number, N was added to these in network2sbml.py
reaction = model.getReaction("N"+name)
if reaction is not None:
law = reaction.createKineticLaw()
if model.getLevel()==2:
lbParameter = law.createParameter()
ubParameter = law.createParameter()
else:
lbParameter = law.createLocalParameter()
ubParameter = law.createLocalParameter()
lbParameter.setId("LOWER_BOUND")
lbParameter.setValue(float(lb))
ubParameter.setId("UPPER_BOUND")
ubParameter.setValue(float(ub))
if(float(ub)>0 and float(lb)<0):
reaction.setReversible(True)
else:
reaction.setReversible(False)
f.close()
libsbml.writeSBMLToFile(document, model_path)
def renameSId (filename, oldSId, newSId, output_file):
if oldSId == newSId:
print("The Ids are identical, renaming stopped.")
return
if not libsbml.SyntaxChecker.isValidInternalSId(newSId):
print("The new SId '{0}' does not represent a valid SId.".format(newSId))
return
document = libsbml.readSBMLFromFile(filename)
errors = document.getNumErrors(libsbml.LIBSBML_SEV_ERROR)
if errors > 0:
document.printErrors()
return
# find elements for old id
element = document.getElementBySId(oldSId)
if element == None:
print("Found no element with SId '{0}'".format(oldSId))
return
# found element -> renaming
element.setId(newSId)
# update all references to this element
allElements = document.getListOfAllElements()
for i in range(allElements.getSize()):
allElements.get(i).renameSIdRefs(oldSId, newSId)
# write to file
libsbml.writeSBMLToFile(document, output_file)
def extract_rxn_with_gene_assoc(sbml, output, verbose=False):
"""
From a given sbml document, create a sbml with only the reactions associated to a gene.
Need for a reaction, in section 'note', 'GENE_ASSOCIATION': ....
Parameters
----------
sbml_file: libsbml.document
sbml document
output: str
pathname of the output sbml
"""
reader = libsbml.SBMLReader()
sbml_document = reader.readSBML(sbml)
for i in range(sbml_document.getNumErrors()):
print(sbml_document.getError(i).getMessage())
sbml_model = sbml_document.getModel()
listOfReactions = sbml_model.getListOfReactions()
reactions_to_remove = []
for reaction in listOfReactions:
if "GENE_ASSOCIATION" not in list(parseNotes(reaction).keys()):
reactions_to_remove.append(reaction.getId())
for rId in reactions_to_remove:
listOfReactions.remove(rId)
libsbml.writeSBMLToFile(sbml_document, output)
def renameSId(filename, oldSId, newSId, output_file):
if oldSId == newSId:
print("The Ids are identical, renaming stopped.")
return
if not libsbml.SyntaxChecker.isValidInternalSId(newSId):
print(
"The new SId '{0}' does not represent a valid SId.".format(newSId))
return
document = libsbml.readSBMLFromFile(filename)
errors = document.getNumErrors(libsbml.LIBSBML_SEV_ERROR)
if errors > 0:
document.printErrors()
return
# find elements for old id
element = document.getElementBySId(oldSId)
if element == None:
print("Found no element with SId '{0}'".format(oldSId))
return
# found element -> renaming
element.setId(newSId)
# update all references to this element
allElements = document.getListOfAllElements()
for i in range(allElements.getSize()):
allElements.get(i).renameSIdRefs(oldSId, newSId)
# write to file
libsbml.writeSBMLToFile(document, output_file)
def add_uncertainty_example(tmp: bool = False) -> None:
"""Add uncertainty to a model."""
doc: libsbml.SBMLDocument = libsbml.readSBMLFromFile(
str(RESOURCES_DIR / "distrib" / "e_coli_core.xml"))
# activate distrib
doc.enablePackage(
"http://www.sbml.org/sbml/level3/version1/distrib/version1", "distrib",
True)
doc.setPackageRequired("distrib", True)
model: libsbml.Model = doc.getModel()
model_fbc: libsbml.FbcModelPlugin = model.getPlugin("fbc")
# write gene expression data
gp = model_fbc.getGeneProduct(0)
gp_distrib: libsbml.DistribSBasePlugin = gp.getPlugin("distrib")
if gp_distrib:
uncertainty: libsbml.Uncertainty = gp_distrib.createUncertainty()
up_mean: libsbml.UncertParameter = uncertainty.createUncertParameter()
up_mean.setType(libsbml.DISTRIB_UNCERTTYPE_MEAN)
up_mean.setValue(2.5)
else:
logger.error("DistribSBasePlugin not working for fbc:GeneProduct.")
# store model with gene expression data
if tmp:
with tempfile.NamedTemporaryFile(suffix=".xml") as f_sbml:
libsbml.writeSBMLToFile(doc, f_sbml.name)
else:
libsbml.writeSBMLToFile(
doc, str(RESOURCES_DIR / "distrib" / "e_coli_core_expression.xml"))
def create_sbml_model(
initial_assignments,
parameters,
rate_rules,
species,
to_file: str = None,
):
"""Create an SBML model from simple definitions.
See the model definitions and usage in :py:func:`model` for example input.
The default initial concentration of species is `1.0`. This can currently
be changed by specifying an initial assignment.
"""
document = libsbml.SBMLDocument(3, 1)
model = document.createModel()
compartment = model.createCompartment()
compartment.setId('compartment')
compartment.setConstant(True)
compartment.setSize(1)
compartment.setSpatialDimensions(3)
compartment.setUnits('dimensionless')
for species_id in species:
species = model.createSpecies()
species.setId(species_id)
species.setCompartment('compartment')
species.setConstant(False)
species.setSubstanceUnits('dimensionless')
species.setBoundaryCondition(False)
species.setHasOnlySubstanceUnits(False)
species.setInitialConcentration(1.0)
for target, formula in initial_assignments.items():
initial_assignment = model.createInitialAssignment()
initial_assignment.setSymbol(target)
initial_assignment.setMath(libsbml.parseL3Formula(formula))
for target, formula in rate_rules.items():
rate_rule = model.createRateRule()
rate_rule.setVariable(target)
rate_rule.setMath(libsbml.parseL3Formula(formula))
for parameter_id, parameter_value in parameters.items():
parameter = model.createParameter()
parameter.setId(parameter_id)
parameter.setConstant(True)
parameter.setValue(parameter_value)
parameter.setUnits('dimensionless')
if to_file:
libsbml.writeSBMLToFile(
document,
str(to_file),
)
# Need to return document, else AMICI throws an error.
# (possibly due to garbage collection?)
return document, model
def setFormulas(self, formulas_path, model_path):
reader = libsbml.SBMLReader()
document = reader.readSBML(model_path)
model = document.getModel()
f = open(formulas_path)
for s in f:
if not s.startswith("#"):
molid, formula = s.strip().split("\t")
species = model.getSpecies(molid)
if species is not None:
note = """
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>FORMULA:%s</p>
</body>
</notes>
""" % (formula.replace(":","").replace(",",""))
if species.isSetNotes():
species.appendNotes(note)
else:
species.setNotes(note)
if not species.isSetNotes():
print "Failed to assign note to %s:\n%s" % (molid,note)
f.close()
libsbml.writeSBMLToFile(document, model_path)
def _adapt_sbml_file(sbml_file):
# create temporary filename for an adapted sbml file for Copasi
temp = sbml_file.split('.')
temp_file_name = temp[0] + '_deleteme.xml'
# get the sbml model, adapt it for Copasi
sbml_model = (libsbml.readSBML(sbml_file)).getModel()
sbml_model_name = sbml_model.getName()
if sbml_model_name == '':
sbml_model_name = (sbml_file.split('.')[0]).split('/')[-1]
sbml_model.setName(sbml_model_name)
output_table = []
for compartment in sbml_model.getListOfCompartments():
# Copasi prioritizes species names over IDs
# We have to remove them to user IDs as identifiers in Copasi
compartment.unsetName()
for species in sbml_model.getListOfSpecies():
# Copasi prioritizes species names over IDs
# We have to remove them to user IDs as identifiers in Copasi
species.unsetMetaId()
species.unsetName()
output_table.append((species.getCompartment(), species.getId()))
# save changed sbml files and the accompaniying sedml file
libsbml.writeSBMLToFile(sbml_model.getSBMLDocument(), temp_file_name)
return temp_file_name, sbml_model_name, output_table
def petab_problem(minimal_sbml_model): # pylint: disable=W0621
"""Test petab problem."""
# create test model
document, model = minimal_sbml_model
p = model.createParameter()
p.setId('fixedParameter1')
p.setName('FixedParameter1')
p = model.createParameter()
p.setId('observable_1')
p.setName('Observable 1')
measurement_df = pd.DataFrame(data={
OBSERVABLE_ID: ['obs1', 'obs2'],
OBSERVABLE_PARAMETERS: ['', 'p1;p2'],
NOISE_PARAMETERS: ['p3;p4', 'p5']
})
condition_df = pd.DataFrame(data={
CONDITION_ID: ['condition1', 'condition2'],
CONDITION_NAME: ['', 'Condition 2'],
'fixedParameter1': [1.0, 2.0]
}).set_index(CONDITION_ID)
parameter_df = pd.DataFrame(data={
PARAMETER_ID: ['dynamicParameter1', 'dynamicParameter2'],
PARAMETER_NAME: ['', '...'],
}).set_index(PARAMETER_ID)
observable_df = pd.DataFrame(data={
OBSERVABLE_ID: ['observable_1'],
OBSERVABLE_NAME: ['julius'],
OBSERVABLE_FORMULA: ['observable_1'],
NOISE_FORMULA: [1],
}).set_index(OBSERVABLE_ID)
with tempfile.TemporaryDirectory() as temp_dir:
sbml_file_name = Path(temp_dir, "model.xml")
libsbml.writeSBMLToFile(document, str(sbml_file_name))
measurement_file_name = Path(temp_dir, "measurements.tsv")
petab.write_measurement_df(measurement_df, measurement_file_name)
condition_file_name = Path(temp_dir, "conditions.tsv")
petab.write_condition_df(condition_df, condition_file_name)
parameter_file_name = Path(temp_dir, "parameters.tsv")
petab.write_parameter_df(parameter_df, parameter_file_name)
observable_file_name = Path(temp_dir, "observables.tsv")
petab.write_observable_df(observable_df, observable_file_name)
yield petab.Problem.from_files(
sbml_file=sbml_file_name,
measurement_file=measurement_file_name,
condition_file=condition_file_name,
parameter_file=parameter_file_name,
observable_files=observable_file_name)
def _process_models(self):
""" Process and prepare models for simulation.
Resolves the replacements and model couplings between the
different frameworks and creates models which can be simulated with
the different frameworks.
An important step is finding the fba rules in the top model.
:return:
:rtype:
"""
logging.debug('* _process_models')
###########################
# FBA rules
###########################
# process FBA assignment rules of the top model
self.flux_rules = DFBAModel._process_flux_rules(self.model_top)
###########################
# ODE model
###########################
# the roadrunner ode file is the flattened comp file.
# FBA parts do not change any of the kinetic subparts (only connections via replaced bounds
# and fluxes).
# Consequently, the ODE part can be solved as is, only the iterative update between ode and fba has
# to be performed
# remove FBA assignment rules from the model, so they can be set via the simulator
# not allowed to set assignment rules directly in roadrunner
for variable in self.flux_rules.values():
self.model_top.removeRuleByVariable(variable)
mixed_sbml_cleaned = tempfile.NamedTemporaryFile("w", suffix=".xml")
libsbml.writeSBMLToFile(self.doc_top, mixed_sbml_cleaned.name)
self.rr_comp = roadrunner.RoadRunner(mixed_sbml_cleaned.name)
###########################
# prepare FBA models
###########################
# FBA models are found based on the FBA modeling framework
mdoc = self.doc_top.getPlugin("comp")
for submodel in self.submodels[builder.MODEL_FRAMEWORK_FBA]:
mref = submodel.getModelRef()
emd = mdoc.getExternalModelDefinition(mref)
source = emd.getSource()
# check if relative path
if not os.path.exists(source):
s2 = os.path.join(self.sbml_dir, source)
if not os.path.exists(s2):
warnings.warn('FBA source cannot be resolved:' + source)
else:
source = s2
# Create FBA model and process
fba_model = FBAModel(submodel=submodel,
source=source,
model_top=self.model_top)
self.fba_models.append(fba_model)
def _process_models(self):
""" Process and prepare models for simulation.
Resolves the replacements and model couplings between the
different frameworks and creates models which can be simulated with
the different frameworks.
An important step is finding the fba rules in the top model.
:return:
:rtype:
"""
logging.debug('* _process_models')
###########################
# FBA rules
###########################
# process FBA assignment rules of the top model
self.flux_rules = DFBAModel._process_flux_rules(self.model_top)
###########################
# ODE model
###########################
# the roadrunner ode file is the flattened comp file.
# FBA parts do not change any of the kinetic subparts (only connections via replaced bounds
# and fluxes).
# Consequently, the ODE part can be solved as is, only the iterative update between ode and fba has
# to be performed
# remove FBA assignment rules from the model, so they can be set via the simulator
# not allowed to set assignment rules directly in roadrunner
for variable in self.flux_rules.values():
self.model_top.removeRuleByVariable(variable)
mixed_sbml_cleaned = tempfile.NamedTemporaryFile("w", suffix=".xml")
libsbml.writeSBMLToFile(self.doc_top, mixed_sbml_cleaned.name)
self.rr_comp = roadrunner.RoadRunner(mixed_sbml_cleaned.name)
###########################
# prepare FBA models
###########################
# FBA models are found based on the FBA modeling framework
mdoc = self.doc_top.getPlugin("comp")
for submodel in self.submodels[builder.MODEL_FRAMEWORK_FBA]:
mref = submodel.getModelRef()
emd = mdoc.getExternalModelDefinition(mref)
source = emd.getSource()
# check if relative path
if not os.path.exists(source):
s2 = os.path.join(self.sbml_dir, source)
if not os.path.exists(s2):
warnings.warn('FBA source cannot be resolved:' + source)
else:
source = s2
# Create FBA model and process
fba_model = FBAModel(submodel=submodel,
source=source,
model_top=self.model_top)
self.fba_models.append(fba_model)
def rxn_kegg2sbml():
kict = get_kegg_data()
sbml = libsbml.SBMLReader().readSBML("Gthg_2.2 (manual).xml")
print('The model has ', sbml.getNumErrors(), ' errors')
model = sbml.getModel()
hypercount = defaultdict(Counter)
for rxn in model.getListOfReactions():
if rxn.getName() in kict:
#Also should add: to RDF
#http://www.kegg.jp/entry/R01090
details = kict[rxn.getName()]
for f in sorted(details):
if f != 'ENTRY':
#How do I encode <=>?
#Unicode? HTML ascii?
#https://en.wikipedia.org/wiki/Arrow_(symbol)
#encode('ascii','xmlcharrefreplace'))
rxn.appendNotes(
'<html:p>' + f + ': ' +
'; '.join(details[f]).replace("<=>", "\u21cc").replace(
'=>', '\u2192').replace('<=', '\u2190') +
'</html:p>')
#if 'DEFINITION' in details and 'EQUATION' in details:
if 'EQUATION' in details:
#Match the species.
#prods=[model.getElementBySId(rxn.getProduct(n).getSpecies()) for n in range(rxn.getNumProducts())]
#reacs=[model.getElementBySId(rxn.getReactant(n).getSpecies()) for n in range(rxn.getNumReactants())]
#Split the def and eq lines and zip then
#terms=list(zip([[re.search("([CG]\d+)",s2).group(0) for s2 in re.sub('\(.*?\)','',s).split('+')] for s in re.split('<?=>?',list(details['EQUATION'])[0])],[s.split('+') for s in re.split('<?=>?',list(details['DEFINITION'])[0])]))
for k in [
re.search("([CG]\d+)", s2).group(0)
for s in re.split('<?=>?',
list(details['EQUATION'])[0])
for s2 in re.sub('\(.*?\)', '', s).split('+')
]:
hypercount[k].update(['Σ'] + [
rxn.getProduct(n).getSpecies()
for n in range(rxn.getNumProducts())
] + [
rxn.getReactant(n).getSpecies()
for n in range(rxn.getNumReactants())
])
else:
print('Unknown ', rxn.getName())
#print(hypercount)
mapID = hyperwinner(hypercount)
print('data:', mapID)
for sp in model.getListOfSpecies():
tag = sp.getId().replace('_e', '_c')
if tag in mapID:
if type(mapID[tag]) is str:
sp.appendNotes('<html:p>KEGG: ' + mapID[tag] + '</html:p>')
#else:
# sp.appendNotes('<html:p>KEGG: either '+' or '.join(mapID[tag])+'</html:p>')
else:
sp.appendNotes('<html:p>KEGG: !!!!GOGGLE IT</html:p>')
print(tag, ' not an id element')
libsbml.writeSBMLToFile(sbml, "test enrich.xml")
def write_ids_to_names(input_path: Path, output_path: Path) -> None:
"""Write SBML ids as names."""
doc: libsbml.SBMLDocument = libsbml.readSBMLFromFile(str(input_path))
elements = doc.getListOfAllElements()
for element in elements:
if element.isSetId():
element.setName(element.id)
libsbml.writeSBMLToFile(doc, str(output_path))
def save(self, filename=None, set_filename=True):
if filename == None:
if self.filename == None:
raise ValueError
else:
filename = self.filename
libsbml.writeSBMLToFile(self.document, filename)
if set_filename == True:
self.filename = filename
def merge_models(model_paths, out_dir=None, merged_id="merged", validate=True):
""" Merge models in model path.
All models must be in the same subfolder.
Relative paths are set in the merged models.
Output directory must exist.
:param model_paths: absolute paths to models
:return:
"""
# necessary to convert models to SBML L3V1
# FIXME: the path should not be changed by functions (this will create problems if run concurrently)
cur_dir = os.getcwd()
os.chdir(out_dir)
base_dir = None
for model_id, path in model_paths.items():
if not os.path.exists(path):
logging.error('Path for SBML file does not exist: {}'.format(path))
# get base dir of all model files from first file
if base_dir is None:
base_dir = os.path.dirname(path)
else:
new_dir = os.path.dirname(path)
if new_dir != base_dir:
raise ValueError('All SBML files for merging must be in same '
'directory: {} != {}'.format(
new_dir, base_dir))
# convert to L3V1
path_L3 = os.path.join(out_dir, "{}_L3.xml".format(model_id))
doc = libsbml.readSBMLFromFile(path)
if doc.getLevel() < SBML_LEVEL:
doc.setLevelAndVersion(SBML_LEVEL, SBML_VERSION)
libsbml.writeSBMLToFile(doc, path_L3)
model_paths[model_id] = path_L3
if validate is True:
for path in model_paths:
validation.check_sbml(path, name=path)
# create comp model
merged_doc = create_merged_doc(model_paths, merged_id=merged_id)
if validate is True:
validation.check_sbml(path, name=path)
# write merged doc
f_out = os.path.join(out_dir, '{}.xml'.format(merged_id))
libsbml.writeSBMLToFile(merged_doc, f_out)
os.chdir(cur_dir)
return merged_doc
def merge_models(model_paths, out_dir=None, merged_id="merged", validate=True):
""" Merge models in model path.
All models must be in the same subfolder.
Relative paths are set in the merged models.
Output directory must exist.
:param model_paths: absolute paths to models
:return:
"""
# necessary to convert models to SBML L3V1
# FIXME: the path should not be changed by functions (this will create problems if run concurrently)
cur_dir = os.getcwd()
os.chdir(out_dir)
base_dir = None
for model_id, path in model_paths.items():
if not os.path.exists(path):
logging.error('Path for SBML file does not exist: {}'.format(path))
# get base dir of all model files from first file
if base_dir is None:
base_dir = os.path.dirname(path)
else:
new_dir = os.path.dirname(path)
if new_dir != base_dir:
raise ValueError('All SBML files for merging must be in same '
'directory: {} != {}'.format(new_dir, base_dir))
# convert to L3V1
path_L3 = os.path.join(out_dir, "{}_L3.xml".format(model_id))
doc = libsbml.readSBMLFromFile(path)
if doc.getLevel() < SBML_LEVEL:
doc.setLevelAndVersion(SBML_LEVEL, SBML_VERSION)
libsbml.writeSBMLToFile(doc, path_L3)
model_paths[model_id] = path_L3
if validate is True:
for path in model_paths:
validation.check_sbml(path, name=path)
# create comp model
merged_doc = create_merged_doc(model_paths, merged_id=merged_id)
if validate is True:
validation.check_sbml(path, name=path)
# write merged doc
f_out = os.path.join(out_dir, '{}.xml'.format(merged_id))
libsbml.writeSBMLToFile(merged_doc, f_out)
os.chdir(cur_dir)
return merged_doc
def sbml_body():
__doc__='SBML2Latex does not like the notes'
sbml=libsbml.SBMLReader().readSBML("Gthg_2.4.xml")
error_check(sbml)
model=sbml.getModel()
for sp in model.getListOfSpecies():
notes='<body xmlns="http://www.w3.org/1999/xhtml">\n'+sp.getNotesString()+'\n</body>'
sp.setNotes(notes.replace('<notes>\n','').replace('</notes>\n','').replace('html:',''))
for rxn in model.getListOfReactions():
notes='<body xmlns="http://www.w3.org/1999/xhtml">\n'+rxn.getNotesString()+'\n</body>'
rxn.setNotes(notes.replace('<notes>\n','').replace('</notes>\n','').replace('html:',''))
libsbml.writeSBMLToFile(sbml,"Gthg_2.4_html_tweak.xml")
def write_ids_to_names(input_path, output_path):
"""
:return:
"""
doc = libsbml.readSBMLFromFile(input_path) # type: libsbml.SBMLDocument
elements = doc.getListOfAllElements()
for element in elements:
if element.isSetId():
element.setName(element.id)
print(element)
libsbml.writeSBMLToFile(doc, output_path)
def write_sbml_to_file(self, sbml_out):
""" Write the SBML file.
First create clean SBML file.
:param sbml_out:
:type sbml_out:
:return:
:rtype:
"""
self._create_sbml()
libsbml.writeSBMLToFile(self.doc, sbml_out)
def addInChiKey(self, input_sbml, output_sbml):
"""Check the MIRIAM annotation for MetaNetX or CHEBI id's and try to recover the inchikey from cache and add it to MIRIAM
:param input_sbml: SBML file input
:param output_sbml: Output SBML file
:type input_sbml: str
:type output_sbml: str
:rtype: bool
:return: Success or failure of the function
"""
filename = input_sbml.split('/')[-1].replace('.rpsbml', '').replace(
'.sbml', '').replace('.xml', '')
self.logger.debug(filename)
rpsbml = rpSBML(inFile=input_sbml)
for spe in rpsbml.getModel().getListOfSpecies():
inchikey = None
miriam_dict = rpsbml.readMIRIAMAnnotation(spe.getAnnotation())
if 'inchikey' in miriam_dict:
self.logger.info('The species ' + str(spe.id) +
' already has an inchikey... skipping')
continue
try:
for mnx in miriam_dict['metanetx']:
inchikey = self.cid_strc[self.rpcache._checkCIDdeprecated(
mnx, self.deprecatedCID_cid)]['inchikey']
if inchikey:
rpsbml.addUpdateMIRIAM(spe, 'species',
{'inchikey': [inchikey]})
else:
self.logger.warning('The inchikey is empty for: ' +
str(spe.id))
continue
except KeyError:
try:
for chebi in miriam_dict['chebi']:
inchikey = self.cid_strc[
self.rpcache._checkCIDdeprecated(
self.chebi_cid[chebi],
self.deprecatedCID_cid)]['inchikey']
if inchikey:
rpsbml.addUpdateMIRIAM(spe, 'species',
{'inchikey': [inchikey]})
else:
self.logger.warning('The inchikey is empty for: ' +
str(spe.id))
continue
except KeyError:
self.logger.warning('Cannot find the inchikey for: ' +
str(spe.id))
writeSBMLToFile(rpsbml.document, output_sbml)
return True
def main (args):
"""Usage: setIdFromNames filename output
"""
if len(args) != 3:
print(main.__doc__)
sys.exit(1)
filename = args[1];
output = args[2];
# read the document
start = time.time() * 1000;
document = libsbml.readSBMLFromFile(filename);
stop = time.time() * 1000;
print ""
print " filename: {0}".format( filename);
print " read time (ms): {0}".format( stop - start);
# stop in case of serious errors
errors = document.getNumErrors(libsbml.LIBSBML_SEV_ERROR);
if (errors > 0):
print " error(s): {0}".format(errors);
document.printErrors();
sys.exit (errors);
# get a list of all elements, as we will need to know all identifiers
# so that we don't create duplicates.
allElements = document.getListOfAllElements();
# get a list of all ids
allIds = getAllIds(allElements);
# create the transformer with the ids
trans = SetIdFromNames(allIds);
# rename the identifiers (using the elements we already gathered before)
start = time.time() * 1000;
document.getModel().renameIDs(allElements, trans);
stop = time.time() * 1000;
print " rename time (ms): {0}".format(stop - start);
# write to file
start = time.time() * 1000;
libsbml.writeSBMLToFile(document, output);
stop = time.time() * 1000;
print " write time (ms): {0}".format(stop - start);
print "";
def main(rdir, eqnfn, molfn, taxon, modelid, modelname, species, outfn):
mol2name = {}
f = open(molfn)
for s in f:
molid, name, name2 = s.strip().split("\t")
mol2name[molid] = name
print "Loading reconstruction: %s/%s" % (rdir, common.NETWORK_REACTION_FILE)
f = open("%s/%s" % (rdir, common.NETWORK_REACTION_FILE))
bf = open(eqnfn)
reco = common.read_reconstruction(f)
eqns = read_balanced_reactions(bf)
print "%d reactions" % (len(reco))
sbml = convert_to_SBML(reco, eqns, mol2name, taxon, modelid, modelname, species)
libsbml.writeSBMLToFile(sbml, outfn)
def create_sbml_file(file_name):
"""
Simple function that creates a new SBML model 'model1' with a non constant parameter x
"""
doc = libsbml.SBMLDocument()
model = doc.createModel()
model.setId('model1')
x = model.createParameter()
x.setId('x')
x.setValue(0)
x.setConstant(False)
libsbml.writeSBMLToFile(doc, file_name)
def main (args):
"""Usage: setIdFromNames filename output
"""
if len(args) != 3:
print(main.__doc__)
sys.exit(1)
filename = args[1];
output = args[2];
# read the document
start = time.time() * 1000;
document = libsbml.readSBMLFromFile(filename);
stop = time.time() * 1000;
print ""
print " filename: {0}".format( filename);
print " read time (ms): {0}".format( stop - start);
# stop in case of serious errors
errors = document.getNumErrors(libsbml.LIBSBML_SEV_ERROR);
if (errors > 0):
print " error(s): {0}".format(errors);
document.printErrors();
sys.exit (errors);
# get a list of all elements, as we will need to know all identifiers
# so that we don't create duplicates.
allElements = document.getListOfAllElements();
# get a list of all ids
allIds = getAllIds(allElements);
# create the transformer with the ids
trans = SetIdFromNames(allIds);
# rename the identifiers (using the elements we already gathered before)
start = time.time() * 1000;
document.getModel().renameIDs(allElements, trans);
stop = time.time() * 1000;
print " rename time (ms): {0}".format(stop - start);
# write to file
start = time.time() * 1000;
libsbml.writeSBMLToFile(document, output);
stop = time.time() * 1000;
print " write time (ms): {0}".format(stop - start);
print "";
def sbml_addkeggchem():
kict = get_kegg_data()
sbml = libsbml.SBMLReader().readSBML("Gthg_2.3.xml")
error_check(sbml)
model = sbml.getModel()
for sp in model.getListOfSpecies():
notes = sp.getNotesString()
regexmatch = re.search('KEGG:\s+(\w+)', notes)
if regexmatch:
cid = regexmatch.group(1)
check(sp.setNotes(notify(cid)), 'species notes')
else:
print('KEGG-less:', notes)
libsbml.writeSBMLToFile(sbml, "test enrich.xml")
def sbml_addkeggchem():
kict=get_kegg_data()
sbml=libsbml.SBMLReader().readSBML("Gthg_2.3.xml")
error_check(sbml)
model=sbml.getModel()
for sp in model.getListOfSpecies():
notes=sp.getNotesString()
regexmatch=re.search('KEGG:\s+(\w+)',notes)
if regexmatch:
cid=regexmatch.group(1)
check(sp.setNotes(notify(cid)),'species notes')
else:
print('KEGG-less:',notes)
libsbml.writeSBMLToFile(sbml,"test enrich.xml")
def process_file(sbml_file):
reader = libsbml.SBMLReader()
doc = reader.readSBML(sbml_file)
model = doc.getModel()
if not model:
return NOT_MODEL, None
model_id = model.getId()
if not model_id:
sbml_name = os.path.splitext(os.path.basename(sbml_file))[0]
model.setId(sbml_name)
model_id = sbml_name
m_id = check_md5(sbml_file)
directory = os.path.join('..', 'html', m_id)
if os.path.exists(directory):
if os.path.exists(os.path.join(directory, 'index.html')):
return ALREADY_EXISTS, (model_id, m_id)
else:
os.makedirs(directory)
copytree(LIB, os.path.join(directory, 'lib'))
log_file = None
try:
log_file = os.path.join(directory, 'log.log')
with open(log_file, "w+"):
pass
except:
pass
logging.basicConfig(level=logging.INFO,
format='%(message)s',
filename=log_file)
if check_for_groups(sbml_file, SBO_CHEMICAL_MACROMOLECULE,
GROUP_TYPE_UBIQUITOUS):
new_sbml_file = os.path.join(directory,
'%s_with_groups.xml' % model_id)
if sbml_file != new_sbml_file:
if not libsbml.writeSBMLToFile(doc, new_sbml_file):
return NOT_MODEL, None
os.remove(sbml_file)
return ALREADY_GENERALIZED, (model_id, model.getName(), m_id)
new_sbml_file = os.path.join(directory, '%s.xml' % model_id)
if sbml_file != new_sbml_file:
if not libsbml.writeSBMLToFile(doc, new_sbml_file):
return NOT_MODEL, None
os.remove(sbml_file)
return OK, (model_id, model.getName(), m_id)
def main(rdir, eqnfn, molfn, taxon, modelid, modelname, species, outfn):
mol2name = {}
f = open(molfn)
for s in f:
molid, name, name2 = s.strip().split("\t")
mol2name[molid] = name
print "Loading reconstruction: %s/%s" % (rdir,
common.NETWORK_REACTION_FILE)
f = open("%s/%s" % (rdir, common.NETWORK_REACTION_FILE))
bf = open(eqnfn)
reco = common.read_reconstruction(f)
eqns = read_balanced_reactions(bf)
print "%d reactions" % (len(reco))
sbml = convert_to_SBML(reco, eqns, mol2name, taxon, modelid, modelname,
species)
libsbml.writeSBMLToFile(sbml, outfn)
def writeSBMLToFile(self, fileName):
"""
Generate SBML from this ReactionNetwork and write it to the given file.
"""
doc = self.getSBMLDocument()
status = libsbml.writeSBMLToFile(doc, fileName)
return status
def test_crn_from_sbml(self):
filename = path.join(input_sbml, "BIOMD0000000001.xml")
output = path.join(input_sbml, "out_BIOMD0000000001.xml")
crn = from_sbml(filename)
success = libsbml.writeSBMLToFile(crn.document, output)
self.assertTrue(success)
def main(rdir, eqnfn, molfn, taxon, modelid, modelname, species, outfn, sbmlversion, boundsfile, rxnnamefile=None, pathwayfile=None):
print("Loading molecule names... ")
# dictionary where keys are mol ids (C00001) and
# items are names from second column of kegg-compounds file
mol2name = common.parse_molecule_names(molfn)
print "Loading reconstruction: %s/%s" % (rdir, common.NETWORK_REACTION_FILE)
f = open("%s/%s" % (rdir, common.NETWORK_REACTION_FILE))
bf = open(eqnfn)
reco = common.read_reconstruction(f)
eqns = read_balanced_reactions(bf)
if pathwayfile is not None:
fp = open(pathwayfile)
pathways={};
pathwayasnames={};
for s in fp:
#print s
sisalto = s.strip().split("\t")
#print len(sisalto)
if len(sisalto)>1:
pathways[sisalto[0]]=sisalto[1]
if len(sisalto)>2:
pathwayasnames[sisalto[0]]=sisalto[2]
if len(pathwayasnames) == 0:
pathwayasnames = None
else:
pathways = None
if rxnnamefile is not None:
fp = open(rxnnamefile)
rxnnames={};
for s in fp:
sisalto = s.strip().split("\t")
if len(sisalto)>1:
rxnnames[sisalto[0]]=sisalto[1]
#print ("rxnnames[%s] = %s" % (sisalto[0],sisalto[1]))
else:
rxnnames = None
bounds={};
if boundsfile is not None:
fp = open(boundsfile)
for s in fp:
sisalto = s.strip().split("\t")
if len(sisalto)>1:
bounds[sisalto[0].strip()]=sisalto[3] +","+ sisalto[4]
# print "%d reactions" % (len(reco))
sbml = convert_to_SBML(reco, eqns, mol2name, taxon, modelid, modelname, species, sbmlversion, bounds, rxnnames, pathways, pathwayasnames)
libsbml.writeSBMLToFile(sbml, outfn)
def test_mass_balance():
doc = libsbml.readSBMLFromFile(data.DEMO_SBML)
# add defaults
fbc.add_default_flux_bounds(doc)
import tempfile
f = tempfile.NamedTemporaryFile('w', suffix='xml')
libsbml.writeSBMLToFile(doc, f.name)
f.flush()
model = cobra.io.read_sbml_model(f.name)
# mass/charge balance
for r in model.reactions:
mb = r.check_mass_balance()
# all metabolites are balanced
assert len(mb) == 0
def annotate_sbml_file(f_sbml, f_annotations, f_sbml_annotated):
"""
Annotate a given SBML file with the provided annotations.
:param f_sbml: SBML to annotation
:param f_annotations: csv file with annotations
:param f_sbml_annotated: annotated file
"""
# read SBML model
doc = libsbml.readSBML(f_sbml)
# read annotations
annotations = ModelAnnotator.annotations_from_file(f_annotations)
doc = annotate_sbml_doc(doc, annotations)
# Save
libsbml.writeSBMLToFile(doc, f_sbml_annotated)
def sbml_body():
__doc__ = 'SBML2Latex does not like the notes'
sbml = libsbml.SBMLReader().readSBML("Gthg_2.4.xml")
error_check(sbml)
model = sbml.getModel()
for sp in model.getListOfSpecies():
notes = '<body xmlns="http://www.w3.org/1999/xhtml">\n' + sp.getNotesString(
) + '\n</body>'
sp.setNotes(
notes.replace('<notes>\n', '').replace('</notes>\n',
'').replace('html:', ''))
for rxn in model.getListOfReactions():
notes = '<body xmlns="http://www.w3.org/1999/xhtml">\n' + rxn.getNotesString(
) + '\n</body>'
rxn.setNotes(
notes.replace('<notes>\n', '').replace('</notes>\n',
'').replace('html:', ''))
libsbml.writeSBMLToFile(sbml, "Gthg_2.4_html_tweak.xml")
def add_exchange_reactions(self, model_path):
DEFAULT_COMPARTMENT = "cytosol"
reader = libsbml.SBMLReader()
document = reader.readSBML(model_path)
model = document.getModel()
print model.getLevel()
for reaction in self.reactions:
## if model contains reactants and products
if self.contains_specie(reaction, model):
r = model.createReaction()
r.setId(reaction.get_id())
r.setMetaId("meta_%s" % (reaction.get_id()))
r.setName(reaction.get_name())
if float(reaction.get_lb()) < 0 and float(reaction.get_ub()) > 0:
r.setReversible(True)
else:
r.setReversible(False)
r.setSBOTerm("SBO:0000176")
r.setFast(False)
r.setCompartment(DEFAULT_COMPARTMENT)
law = r.createKineticLaw()
if model.getLevel()==2:
lbParameter = law.createParameter()
ubParameter = law.createParameter()
else:
lbParameter = law.createLocalParameter()
ubParameter = law.createLocalParameter()
lbParameter.setId("LOWER_BOUND")
lbParameter.setValue(float(reaction.get_lb()))
ubParameter.setId("UPPER_BOUND")
ubParameter.setValue(float(reaction.get_ub()))
for reactant in reaction.get_reactants():
re = r.createReactant()
re.setSpecies(reactant.get_id())
re.setStoichiometry(float(reactant.get_stoichiometry()))
re.setConstant(True)
for product in reaction.get_products():
pr = r.createProduct()
pr.setSpecies(product.get_id())
pr.setStoichiometry(float(product.get_stoichiometry()))
pr.setConstant(True)
libsbml.writeSBMLToFile(document, model_path)
def process_file(sbml_file):
reader = libsbml.SBMLReader()
doc = reader.readSBML(sbml_file)
model = doc.getModel()
if not model:
return NOT_MODEL, None
model_id = model.getId()
if not model_id:
sbml_name = os.path.splitext(os.path.basename(sbml_file))[0]
model.setId(sbml_name)
model_id = sbml_name
m_id = check_md5(sbml_file)
directory = os.path.join("..", "html", m_id)
if os.path.exists(directory):
if os.path.exists(os.path.join(directory, "index.html")):
return ALREADY_EXISTS, (model_id, m_id)
else:
os.makedirs(directory)
copytree(LIB, os.path.join(directory, "lib"))
log_file = None
try:
log_file = os.path.join(directory, "log.log")
with open(log_file, "w+"):
pass
except:
pass
logging.basicConfig(level=logging.INFO, format="%(message)s", filename=log_file)
if check_for_groups(sbml_file, SBO_CHEMICAL_MACROMOLECULE, GROUP_TYPE_UBIQUITOUS):
new_sbml_file = os.path.join(directory, "%s_with_groups.xml" % model_id)
if sbml_file != new_sbml_file:
if not libsbml.writeSBMLToFile(doc, new_sbml_file):
return NOT_MODEL, None
os.remove(sbml_file)
return ALREADY_GENERALIZED, (model_id, model.getName(), m_id)
new_sbml_file = os.path.join(directory, "%s.xml" % model_id)
if sbml_file != new_sbml_file:
if not libsbml.writeSBMLToFile(doc, new_sbml_file):
return NOT_MODEL, None
os.remove(sbml_file)
return OK, (model_id, model.getName(), m_id)
def __init__(self, modelPath, reactionPath, biomassPath, boundsPath, exchange, outputPath):
self.reactions = []
self.model =''
if(modelPath):
#read model
reader = libsbml.SBMLReader()
document = reader.readSBML(modelPath)
self.model = document.getModel()
newDocument = document.clone();
if(reactionPath):
self.parseReactionBag(reactionPath)
if self.model == None:
return
listOfReactions = self.model.getListOfReactions()
for reaction in self.reactions:
if not reaction.isInModel(listOfReactions):
print "adding Reaction:" + reaction.getId()
else:
print "the reaction " + reaction.getId() + " is already on the model. OverWriting..."
self.model.getReaction(reaction.getOverReaction()).removeFromParentAndDelete()
self.addReactionInToModel(reaction, self.model)
if(biomassPath):
print "adding biomass Reaction"
reaction = self.parseBiomass(biomassPath)
if not reaction.isInModel(self.model.getListOfReactions()):
self.addReactionInToModel(reaction, self.model)
if(boundsPath):
print "adding new bounds"
self.parseBounds(boundsPath, self.model)
if(exchange):
print "adding exchage reactions"
self.addExchangeReactions(self.model)
if(outputPath):
print "Writing file"
newDocument.setModel(self.model)
libsbml.writeSBMLToFile(newDocument, outputPath)
def sbml_rdf_fixer():
__doc__='Too hard to workout. Abbanded.'
sbml=libsbml.SBMLReader().readSBML("Gthg_2.4.xml")
error_check(sbml)
model=sbml.getModel()
for sp in model.getListOfSpecies():
if not sp.getCVTerms():
print(sp.addCVTerm(libsbml.CVTerm(libsbml.BIOLOGICAL_QUALIFIER), True))
bag=sp.getCVTerm(0)
notes=sp.getNotesString()
regexmatch=re.search('CHEBI:\s+(.*?)[<;]',notes)
if regexmatch:
name=regexmatch.group(1)
bag.addResource("urn:miriam:chebi:CHEBI%3A"+name)
regexmatch=re.search('KEGG:\s+(.*?)[<;]',notes)
if regexmatch:
name=regexmatch.group(1)
bag.addResource("urn:miriam:kegg.compound:"+name)
libsbml.writeSBMLToFile(sbml,"test enrich.xml")
def rxn_kegg2sbml():
kict=get_kegg_data()
sbml=libsbml.SBMLReader().readSBML("Gthg_2.2 (manual).xml")
print('The model has ',sbml.getNumErrors(),' errors')
model=sbml.getModel()
hypercount=defaultdict(Counter)
for rxn in model.getListOfReactions():
if rxn.getName() in kict:
#Also should add: to RDF
#http://www.kegg.jp/entry/R01090
details=kict[rxn.getName()]
for f in sorted(details):
if f !='ENTRY':
#How do I encode <=>?
#Unicode? HTML ascii?
#https://en.wikipedia.org/wiki/Arrow_(symbol)
#encode('ascii','xmlcharrefreplace'))
rxn.appendNotes('<html:p>'+f+': '+'; '.join(details[f]).replace("<=>","\u21cc").replace('=>','\u2192').replace('<=','\u2190')+'</html:p>')
#if 'DEFINITION' in details and 'EQUATION' in details:
if 'EQUATION' in details:
#Match the species.
#prods=[model.getElementBySId(rxn.getProduct(n).getSpecies()) for n in range(rxn.getNumProducts())]
#reacs=[model.getElementBySId(rxn.getReactant(n).getSpecies()) for n in range(rxn.getNumReactants())]
#Split the def and eq lines and zip then
#terms=list(zip([[re.search("([CG]\d+)",s2).group(0) for s2 in re.sub('\(.*?\)','',s).split('+')] for s in re.split('<?=>?',list(details['EQUATION'])[0])],[s.split('+') for s in re.split('<?=>?',list(details['DEFINITION'])[0])]))
for k in [re.search("([CG]\d+)",s2).group(0) for s in re.split('<?=>?',list(details['EQUATION'])[0]) for s2 in re.sub('\(.*?\)','',s).split('+')]:
hypercount[k].update(['Σ']+[rxn.getProduct(n).getSpecies() for n in range(rxn.getNumProducts())]+[rxn.getReactant(n).getSpecies() for n in range(rxn.getNumReactants())])
else:
print('Unknown ',rxn.getName())
#print(hypercount)
mapID=hyperwinner(hypercount)
print('data:',mapID)
for sp in model.getListOfSpecies():
tag=sp.getId().replace('_e','_c')
if tag in mapID:
if type(mapID[tag]) is str:
sp.appendNotes('<html:p>KEGG: '+mapID[tag]+'</html:p>')
#else:
# sp.appendNotes('<html:p>KEGG: either '+' or '.join(mapID[tag])+'</html:p>')
else:
sp.appendNotes('<html:p>KEGG: !!!!GOGGLE IT</html:p>')
print(tag,' not an id element')
libsbml.writeSBMLToFile(sbml,"test enrich.xml")
def test_crn_from_react_file(self):
reactions = parse_reaction_file(path.join(input_reactions, "allosteric_activation"))
filename = path.join(input_sbml, "allosteric_activation.xml")
model, document, _ = model_from_reacts(reactions)
success = libsbml.writeSBMLToFile(document, filename)
self.assertTrue(success)
crn = from_sbml(filename)
crn.inspect()
def add_timecourse_as_events(
petab_problem: petab.Problem,
#sbml_path: TYPE_PATH,
timecourse_id: str = None,
output_path: Optional[TYPE_PATH] = None,
):
#sbml_path = str(sbml_path)
#if output_path is None:
# output_path = sbml_path
#output_path = str(output_path)
if timecourse_id is None:
try:
timecourse_id = one(petab_problem.timecourse_df.index)
except ValueError:
raise ValueError(
'A timecourse ID must be specified if there are multiple '
'timecourses in the PEtab problem timecourse table.')
#sbml_document = libsbml.SBMLReader().readSBML(sbml_path)
sbml_model = petab_problem.sbml_document.getModel()
#if sbml_model is None:
# raise ValueError(
# 'An SBML model could not be reproduced from the SBML file.'
# )
timecourse = parse_timecourse_string(
petab_problem.timecourse_df.loc[timecourse_id][TIMECOURSE], )
for time, condition_id in timecourse:
add_event(
sbml_model=sbml_model,
event_id=get_slug(time),
trigger_formula=f'time >= {time}',
event_assignments=Condition(
petab_problem.condition_df.loc[condition_id], ),
)
if output_path is not None:
libsbml.writeSBMLToFile(sbml_document, str(output_path))
return sbml_model
def prepare_rbc_model(model_path, name, target_dir):
""" Add ports to the RBC model.
:param model_path:
:param name:
:param target_dir:
:return:
"""
doc = libsbml.readSBMLFromFile(model_path) # type: libsbml.SBMLDocument
# add comp package
# sbmlns = libsbml.SBMLNamespaces(doc.getLevel(), doc.getVersion())
# sbmlns.addPackageNamespace("comp", 1)
doc.enablePackage("http://www.sbml.org/sbml/level3/version1/comp/version1",
"comp", True)
# doc.setNamespaces(sbmlns)
doc.setPackageRequired("comp", True)
model = doc.getModel()
model.setId(name)
print(model)
cmodel = model.getPlugin("comp") # type: libsbml.CompModelPlugin
def create_port(sid):
"""" Creates port for given SBase ID."""
p = cmodel.createPort() # type: libsbml.Port
port_sid = f'{sid}{PORT_SUFFIX}'
p.setId(port_sid)
p.setName(port_sid)
p.setMetaId(port_sid)
p.setSBOTerm(599) # port
p.setIdRef(sid)
return p
# add ports
cmodel = model.getPlugin("comp") # type: libsbml.CompModelPlugin
for sid in ['Vplasma', 'glcEXT', 'lacEXT', 'phosEXT', 'pyrEXT']:
create_port(sid)
output_path = os.path.join(target_dir, "{}.xml".format(name))
libsbml.writeSBMLToFile(doc, output_path)
return output_path
def _create_sbml(self):
""" Create the SBMLDocument.
:return:
:rtype:
"""
self._init_sbml_model()
self.interpolators = Interpolation.create_interpolators(
self.data, self.method)
for interpolator in self.interpolators:
Interpolation.add_interpolator_to_model(interpolator, self.model)
# validation of SBML document
try:
temp_dir = tempfile.mkdtemp()
tmp_f = os.path.join(temp_dir, 'validated.xml')
libsbml.writeSBMLToFile(self.doc, tmp_f)
validation.check_sbml(tmp_f, ucheck=False)
finally:
shutil.rmtree(temp_dir)
def add_uncertainty_example(tmp: bool = False) -> None:
"""Add uncertainty to a model."""
output_dir = str(Path(__file__).parent)
doc = libsbml.readSBMLFromFile(os.path.join(
output_dir, "e_coli_core.xml")) # type: libsbml.SBMLDocument
# activate distrib
doc.enablePackage(
"http://www.sbml.org/sbml/level3/version1/distrib/version1", "distrib",
True)
doc.setPackageRequired("distrib", True)
model = doc.getModel() # type: libsbml.Model
model_fbc = model.getPlugin("fbc") # type: libsbml.FbcModelPlugin
# --------------------------------
# [2] write gene expression data
# --------------------------------
gp = model_fbc.getGeneProduct(0)
print(gp)
gp_distrib = gp.getPlugin("distrib") # type: libsbml.DistribSBasePlugin
print(gp_distrib)
if gp_distrib:
uncertainty = gp_distrib.createUncertainty(
) # type: libsbml.Uncertainty
up_mean = uncertainty.createUncertParameter(
) # type: libsbml.UncertParameter
up_mean.setType(libsbml.DISTRIB_UNCERTTYPE_MEAN)
up_mean.setValue(2.5)
else:
logging.error("DistribSBasePlugin not working for fbc:GeneProduct.")
# store model with gene expression data
if tmp:
with tempfile.NamedTemporaryFile(suffix=".xml") as f_sbml:
libsbml.writeSBMLToFile(doc, f_sbml.name)
else:
libsbml.writeSBMLToFile(
doc, os.path.join(output_dir, "e_coli_core_expression.xml"))
def sbml_rdf_fixer():
__doc__ = 'Too hard to workout. Abbanded.'
sbml = libsbml.SBMLReader().readSBML("Gthg_2.4.xml")
error_check(sbml)
model = sbml.getModel()
for sp in model.getListOfSpecies():
if not sp.getCVTerms():
print(
sp.addCVTerm(libsbml.CVTerm(libsbml.BIOLOGICAL_QUALIFIER),
True))
bag = sp.getCVTerm(0)
notes = sp.getNotesString()
regexmatch = re.search('CHEBI:\s+(.*?)[<;]', notes)
if regexmatch:
name = regexmatch.group(1)
bag.addResource("urn:miriam:chebi:CHEBI%3A" + name)
regexmatch = re.search('KEGG:\s+(.*?)[<;]', notes)
if regexmatch:
name = regexmatch.group(1)
bag.addResource("urn:miriam:kegg.compound:" + name)
libsbml.writeSBMLToFile(sbml, "test enrich.xml")
def test_biomodel_merge():
""" Test model merging.
Using the pytest tmpdir fixture
:param tmpdir:
:return:
"""
manipulation_dir = os.path.join(data_dir, 'manipulation')
# dictionary of ids & paths of models which should be combined
# here we just bring together the first Biomodels
model_ids = ["BIOMD000000000{}".format(k) for k in range(1, 5)]
model_paths = dict(zip(model_ids,
[os.path.join(manipulation_dir, "{}.xml".format(mid)) for mid in model_ids])
)
print(model_paths)
# merge model
out_dir = os.path.join(manipulation_dir, 'output')
if not os.path.exists(out_dir):
os.mkdir(out_dir)
print('out_dir:', out_dir)
doc = manipulation.merge_models(model_paths, out_dir=out_dir, validate=False)
assert doc is not None
Nall, Nerr, Nwarn = validation.check_doc(doc, ucheck=False)
assert Nerr == 0
assert Nwarn == 0
assert Nall == 0
# flatten the model
doc_flat = comp.flattenSBMLDocument(doc)
assert doc_flat is not None
libsbml.writeSBMLToFile(doc_flat, os.path.join(out_dir, "merged_flat.xml"))
Nall, Nerr, Nwarn = validation.check_doc(doc_flat, ucheck=False)
assert Nerr == 0
assert Nwarn in [0, 74]
assert Nall in [0, 74]
def create_sbml_report(sbml_path, out_dir, template='report.html', promote=False, validate=True):
""" Creates the SBML report in the out_dir
:param validate:
:param promote:
:param template:
:param sbml_path:
:param doc:
:param out_dir:
:return:
:rtype:
"""
# check if sbml_file exists
if not os.path.exists(sbml_path):
warnings.warn('SBML file does not exist: {}'.format(sbml_path))
# check sbml file
if validate:
check_sbml(sbml_path)
# read sbml
doc = libsbml.readSBML(sbml_path)
if promote:
promote_local_variables(doc)
# write sbml to output folder
basename = os.path.basename(sbml_path)
tokens = basename.split('.')
name = '.'.join(tokens[:-1])
f_sbml = os.path.join(out_dir, basename)
libsbml.writeSBMLToFile(doc, f_sbml)
# write html (unicode)
html = _create_html(doc, basename, html_template=template)
f_html = codecs.open(os.path.join(out_dir, '{}.html'.format(name)),
encoding='utf-8', mode='w')
f_html.write(html)
f_html.close()
def example(path):
"""
Example FBA with demo model.
:param path:
:type path:
:return:
:rtype:
"""
doc = libsbml.readSBMLFromFile(path)
# add defaults
fbc.add_default_flux_bounds(doc)
import tempfile
f = tempfile.NamedTemporaryFile('w', suffix='xml')
libsbml.writeSBMLToFile(doc, f.name)
f.flush()
model = cobra.io.read_sbml_model(f.name)
# mass/charge balance
for r in model.reactions:
mb = r.check_mass_balance()
print(r.id, mb)
parser.add_argument('--metabolite-id', dest="metabolite_id", default="name", action='store', help="Strategy to generate unique metabolite id. Specify 'name' to use metabolite name as SBML id or 'auto' to use auto-incrementing id M_XXXX. (default: name)")
parser.add_argument('--compartment-id', dest="compartment_id", default="name", action='store', help="Strategy to generate unique compartment id. Specify 'name' to use compartment name as SBML id or 'auto' to use auto-incrementing id C_XXXX. (default: name)")
parser.add_argument('--metabolite-map', dest="metabolite_map", action='store', help="Map metabolite identifiers to names")
args = parser.parse_args()
# Read bioopt model
parser = BiooptParser(inf=args.in_inf)
model = parser.parse_file(args.bioopt)
metabolite_map = {}
if args.metabolite_map:
for i, line in enumerate(open(args.metabolite_map)):
l = re.split("\t", line.rstrip())
if len(l) >= 2:
metabolite_map[l[0]] = l[1]
else:
raise RuntimeError("Error on line {} in '{}' file. Map file should have more than 2 columns".format(i, args.metabolite_map))
converter = Bioopt2SbmlConverter(level=args.level, version=args.version,
compartment_pattern=args.c_pattern, inf=args.out_inf, metabolite_map=metabolite_map,
reaction_id=args.reaction_id, metabolite_id=args.metabolite_id, compartment_id=args.compartment_id)
sbml = converter.convert(model)
libsbml.writeSBMLToFile(sbml, args.sbml)
print "Finished converting {0} into SBML ({1})".format(args.bioopt, args.sbml)
# setting because it is required (if unlucky additional info required)
# but we can't set it because we can't access the FBCModelPlugins of the ModelDefinitions
if fbc_model is not None:
if not fbc_model.isSetStrict():
fbc_model.setStrict(False)
else:
print("WARNING: This should never happen. All ModelDefinitions should have a FBCModelPlugin")
doc.checkInternalConsistency()
doc.printErrors()
return doc
if __name__ == "__main__":
import libsbml
from os.path import join as pjoin
directory = './emd_files/'
top_file = pjoin(directory, 'diauxic_top.xml')
# replace the ExternalModelDefinitions with ModelDefinitions
doc_top = libsbml.readSBMLFromFile(top_file)
doc_no_emd = flattenExternalModelDefinitions(doc_top)
# write to file
libsbml.writeSBMLToFile(doc_no_emd, pjoin(directory, 'test_emd_flat.xml'))
print(libsbml.__version__)
def save_as_sbml(input_model, out_sbml):
logging.info("saving to {0}".format(out_sbml))
out_doc = libsbml.SBMLDocument(input_model.getSBMLNamespaces())
out_doc.setModel(input_model)
libsbml.writeSBMLToFile(out_doc, out_sbml)
def simple_merge_models(S, model_id2c_id2group, model_id2dfs, out_sbml):
doc = libsbml.SBMLDocument(2, 4)
model = doc.createModel()
model.setId('merged_model')
model_id2id2id = defaultdict(dict)
common_ids = set()
c_group2id = {}
new_m_id2i, new_r_id2i, new_efm_id2i, new_boundary_m_ids = {}, {}, {}, []
for model_id, [_, _, df] in model_id2dfs.items():
for index, row in df.iterrows():
c_id, name = row['Id'], row['Name']
if model_id in model_id2c_id2group and c_id in model_id2c_id2group[model_id]:
group = model_id2c_id2group[model_id][c_id]
if group in c_group2id:
new_id = c_group2id[group]
else:
new_id = create_compartment(model, name=name, id_='merged_%s_%s' % (model_id, c_id)).getId()
c_group2id[group] = new_id
common_ids.add(new_id)
else:
new_id = create_compartment(model, name=name, id_='%s_%s' % (model_id, c_id)).getId()
model_id2id2id[model_id][c_id] = new_id
id2id = {}
m_id_group_ids = set(S.m_id2gr_id.values())
for (model_id, m_id), i in ((it, i) for (it, i) in S.m_id2i.items() if it not in m_id_group_ids):
c_id = model_id2dfs[model_id][0].at[m_id, 'Compartment']
c_id = model_id2id2id[model_id][c_id]
name = model_id2dfs[model_id][0].at[m_id, 'Name']
is_boundary = (model_id, m_id) in S.boundary_m_ids
new_id = create_species(model, compartment_id=c_id, name=name, bound=is_boundary,
id_='%s_%s' % (model_id, m_id)).getId()
model_id2id2id[model_id][m_id] = new_id
id2id[(model_id, m_id)] = new_id
new_m_id2i[new_id] = i
if is_boundary:
new_boundary_m_ids.append(new_id)
for it in m_id_group_ids:
model_id, m_ids = next(iter(it))
m_id = next(iter(m_ids))
is_boundary = it in S.boundary_m_ids
new_id = \
create_species(model,
compartment_id=model_id2id2id[model_id][model_id2dfs[model_id][0].at[m_id, 'Compartment']],
name=model_id2dfs[model_id][0].at[m_id, 'Name'], bound=is_boundary,
id_='merged_%s_%s' % (model_id, m_id)).getId()
for model_id, m_ids in it:
model_id2id2id[model_id].update({m_id: new_id for m_id in m_ids})
id2id[it] = new_id
new_m_id2i[new_id] = S.m_id2i[it]
if is_boundary:
new_boundary_m_ids.append(new_id)
common_ids.add(new_id)
for ((model_id, r_id), i) in ((it, i) for (it, i) in S.r_id2i.items() if it not in S.gr_id2r_id2c.keys()):
r_id2st, p_id2st = S.st_matrix.get_inputs_outputs((model_id, r_id))
new_id = create_reaction(model, {id2id[m_id]: st for (m_id, st) in r_id2st.items()},
{id2id[m_id]: st for (m_id, st) in p_id2st.items()},
model_id2dfs[model_id][1].at[r_id, 'Name'], reversible=True,
id_='%s_%s' % (model_id, r_id)).getId()
model_id2id2id[model_id][r_id] = new_id
new_r_id2i[new_id] = i
for gr, it2c in S.gr_id2r_id2c.items():
model_id, r_id = next(iter(it2c.keys()))
r_id2st, p_id2st = S.st_matrix.get_inputs_outputs(gr)
new_id = \
create_reaction(model, {id2id[m_id]: st for (m_id, st) in r_id2st.items()},
{id2id[m_id]: st for (m_id, st) in p_id2st.items()},
model_id2dfs[model_id][1].at[r_id, 'Name'], reversible=True,
id_='merged_%s_%s' % (model_id, r_id)).getId()
for model_id, r_id in it2c.keys():
model_id2id2id[model_id][r_id] = new_id
new_r_id2i[new_id] = S.r_id2i[gr]
common_ids.add(new_id)
for ((model_id, efm_id), i) in ((it, i) for (it, i) in S.efm_id2i.items() if it not in S.gr_id2efm_ids.keys()):
new_id = '%s_%s' % (model_id, efm_id)
new_efm_id2i[new_id] = i
model_id2id2id[model_id][efm_id] = new_id
for gr, efm_ids in S.gr_id2efm_ids.items():
model_id, efm_id = next(efm_ids)
new_id = 'merged_%s_%s' % (model_id, efm_id)
new_efm_id2i[new_id] = S.r_id2i[gr]
for model_id, efm_id in efm_ids:
model_id2id2id[model_id][efm_id] = new_id
libsbml.writeSBMLToFile(doc, out_sbml)
return model_id2id2id, common_ids, System(m_id2i=new_m_id2i, r_id2i=new_r_id2i, efm_id2i=new_efm_id2i, N=S.N, V=S.V,
boundary_m_ids=new_boundary_m_ids)
# success probability of Geometric-1
up_mean_geo1 = up.createUncertParameter() # type: libsbml.UncertParameter
up_mean_geo1.setType(libsbml.DISTRIB_UNCERTTYPE_EXTERNALPARAMETER)
up_mean_geo1.setName("success probability of Geometric 1")
up_mean_geo1.setValue(0.4)
up_mean_geo1.setDefinitionURL("http://www.probonto.org/ontology#PROB_k0000789")
return doc
if __name__ == "__main__":
functions = [
# distrib_normal,
# distrib_all,
uncertainty,
]
for f_creator in functions:
name = f_creator.__name__
print(name)
# distrib_example1()
doc = f_creator()
sbml = libsbml.writeSBMLToString(doc)
print("-" * 80)
print(sbml)
print("-" * 80)
sbml_path = "./{}.xml".format(name)
libsbml.writeSBMLToFile(doc, sbml_path)
validation.check_doc(doc)
if not os.path.isfile( ANN_FILE_PATH):
logging.getLogger( "st2sbml").error( "input {0} does not exist or is not a file".format( ANN_FILE_PATH))
exit(1)
TRIGGER, ENTITY_TRIGGER, EVENTS = parse_standoff.parse_ann( ANN_FILE_PATH);
else:
A1_FILE_PATH = CMD_ARGS.path + CMD_ARGS.a1
A2_FILE_PATH = CMD_ARGS.path + CMD_ARGS.a2
logging.getLogger( "st2sbml").info( "Processing %s a1/a2", CMD_ARGS.path)
if not os.path.isfile( A1_FILE_PATH):
logging.getLogger( "st2sbml").error( "Input %s does not exist or is not a file", A1_FILE_PATH)
exit(1)
if not os.path.isfile( A2_FILE_PATH):
logging.getLogger( "st2sbml").error( "Input %s does not exist or is not a file", A2_FILE_PATH)
exit(1)
# parse the a1/a2 files
TRIGGER, ENTITY_TRIGGER, EVENTS = parse_standoff.parse_a1_a2( A1_FILE_PATH, A2_FILE_PATH);
else:
ANN_FILE_PATH = CMD_ARGS.file
logging.getLogger( "st2sbml").info( "Processing %s", ANN_FILE_PATH)
if not os.path.isfile( ANN_FILE_PATH):
logging.getLogger( "st2sbml").error( "input {0} does not exist or is not a file".format( ANN_FILE_PATH))
exit(1)
TRIGGER, ENTITY_TRIGGER, EVENTS = parse_standoff.parse_ann( ANN_FILE_PATH);
logging.getLogger( "st2sbml").info( "Processing {}: loaded {} entity trigger and {} events".format( CMD_ARGS.path, len(ENTITY_TRIGGER), len( EVENTS.keys())))
DOCUMENT = create_document( trigger = TRIGGER, entity_trigger = ENTITY_TRIGGER, events = EVENTS, arguments = CMD_ARGS)
##### WRITE SBML FILE
libsbml.writeSBMLToFile( DOCUMENT, CMD_ARGS.output)
gpr_dict[cols[1]] = cols[4]
infile = '/Users/wbryant/Dropbox/UG Project - COGzymes/model data/BTH_iah991.xml'
reader = SBMLReader()
document = reader.readSBMLFromFile(infile)
model = document.getModel()
notes_string = ' <body xmlns="http://www.w3.org/1999/xhtml">\n <p>GENE_ASSOCIATION: %s</p>\n </body>'
for reaction in model.getListOfReactions():
id_rxn = reaction.getId()
id_rxn = re.sub("^R_","",id_rxn)
id_rxn = re.sub("_LPAREN_","(",id_rxn)
id_rxn = re.sub("_RPAREN_",")",id_rxn)
id_rxn = re.sub("_DASH_","-",id_rxn)
if id_rxn in gpr_dict:
gpr = gpr_dict[id_rxn]
else:
print('%s not found ...' % id_rxn)
gpr = ''
gpr_string = notes_string % gpr
reaction.setNotes(gpr_string)
document.setModel(model)
writeSBMLToFile(document,'BTH_with_gprs.xml')
import tesbml as libsbml
doc = libsbml.SBMLDocument(3, 2)
model = doc.createModel()
model.id = "test_inline_unit"
ud = model.createUnitDefinition()
ud.setId("m")
u = model.createUnit()
u.setKind(libsbml.UNIT_KIND_METRE)
u.setExponent(1.0)
u.setScale(1)
u.setMultiplier(1.0)
ud.addUnit(u)
p = model.createParameter()
p.id = "p"
p.constant = False
p.units = "m"
rule = model.createAssignmentRule()
rule.variable = "p"
ast = libsbml.parseL3FormulaWithModel("5.0 m", model)
rule.setMath(ast)
formula = libsbml.formulaToL3String(ast)
print(formula)
libsbml.writeSBMLToFile(doc, "/home/mkoenig/Desktop/inline_units_py.xml")
def flattenSBMLDocument(doc, leave_ports=True, output_path=None, suffix='_flat'):
""" Flatten the given SBMLDocument.
Validation should be performed before the flattening and is not part
of the flattening routine.
:param doc: SBMLDocument to flatten.
:type doc: SBMLDocument
:return:
:rtype: SBMLDocument
"""
Nerrors = doc.getNumErrors()
if Nerrors > 0:
if doc.getError(0).getErrorId() == libsbml.XMLFileUnreadable:
# Handle case of unreadable file here.
logging.error("SBML error in doc: libsbml.XMLFileUnreadable")
elif doc.getError(0).getErrorId() == libsbml.XMLFileOperationError:
# Handle case of other file error here.
logging.error("SBML error in doc: libsbml.XMLFileOperationError")
else:
# Handle other error cases here.
logging.error("SBML errors in doc, see SBMLDocument error log.")
# converter options
props = libsbml.ConversionProperties()
props.addOption("flatten comp", True) # Invokes CompFlatteningConverter
props.addOption("leave_ports", leave_ports) # Indicates whether to leave ports
# flatten
current = time.clock()
result = doc.convert(props)
flattened_status = (result==libsbml.LIBSBML_OPERATION_SUCCESS)
lines = [
'',
'-' * 120,
str(doc),
"{:<25}: {}".format("flattened", str(flattened_status).upper()),
"{:<25}: {:.3f}".format("flatten time (ms)", time.clock() - current),
'-' * 120,
]
info = "\n".join(lines)
if flattened_status:
logging.info(info)
else:
logging.error(info)
raise ValueError("SBML could not be flattend due to errors in the SBMLDocument.")
if suffix is not None:
model = doc.getModel()
if model is not None:
model.setId(model.getId() + suffix)
if model.isSetName():
model.setName(model.getName() + suffix)
if output_path is not None:
# Write the results to the output file.
libsbml.writeSBMLToFile(doc, output_path)
logging.info("Flattened model written to {}".format(output_path))
return doc
def simulate(mixed_sbml, tend=10.0, step_size=0.1, debug=False):
"""
Performs model simulation.
The simulator figures out based on the SBO terms in the list of submodels, which
simulation/modelling framework to use.
The passing of information between FBA and SSA/ODE is based on the list of replacements.
:param mixed_sbml: comp sbml model with multiple submodels
:param tend: end time of the simulation
:param step_size: step size for the integration, if None variable step size will be used
:param debug: additional information
:return: pandas solution data frame
"""
###############################
# Process FBA assignment rules
###############################
# Necessary to find the assignment rules in the top model
# These cannot be set in an hybrid approach.
doc = libsbml.readSBMLFromFile(mixed_sbml)
model = doc.getModel()
def _process_mixed_assignments(model):
"""
Find the assignment rules which assign to a variable a reaction rate.
"""
fba_rules = {}
for rule in model.getListOfRules():
if not rule.isAssignment():
continue
variable = rule.getVariable()
formula = rule.getFormula()
parameter = model.getParameter(variable)
if not parameter:
continue
reaction = model.getReaction(formula)
if not reaction:
continue
fba_rules[reaction.getId()] = parameter.getId()
return fba_rules
fba_rules = _process_mixed_assignments(model)
print('FBA rules:', fba_rules)
# remove the FBA assignment rules from the model, so they can be set via the simulator
for variable in fba_rules.values():
print(variable)
model.removeRuleByVariable(variable)
import tempfile
mixed_sbml_cleaned = tempfile.NamedTemporaryFile("w", suffix=".xml")
libsbml.writeSBMLToFile(doc, mixed_sbml_cleaned.name)
# mixed_sbml_cleaned.close()
###########################
# Load ODE model
###########################
# the roadrunner ode file is the flattend comp file.
# FBA subparts do not change change any of the kinetic subparts (only connections via replaced bounds
# and fluxes).
# Consequently the ode part can be solved as is, only the iterative update between ode and fba has
# to be performed
rr_comp = roadrunner.RoadRunner(mixed_sbml_cleaned.name)
sel = ['time'] \
+ ["".join(["[", item, "]"]) for item in rr_comp.model.getBoundarySpeciesIds()] \
+ ["".join(["[", item, "]"]) for item in rr_comp.model.getFloatingSpeciesIds()] \
+ rr_comp.model.getReactionIds() + fba_rules.values()
rr_comp.timeCourseSelections = sel
rr_comp.reset()
###########################
# Load FBA models
###########################
# via the submodels information it is decided which submodels are belonging to which
# modeling framework (SBOTerms on submodel)
doc = libsbml.readSBMLFromFile(mixed_sbml)
model_frameworks = comp.get_submodel_frameworks(doc)
model = doc.getModel()
# get top level reaction ids
# top_level_rids = frozenset([reaction.getId() for reaction in model.getListOfReactions()])
# assign submodels to FBA
fba_models = {}
for key, value in model_frameworks.iteritems():
if value["sbo"] == 624:
print('FBA model')
# get SBML file
modelRef = value["modelRef"]
mdoc = doc.getPlugin("comp")
emd = mdoc.getExternalModelDefinition(modelRef)
source = emd.getSource()
print(source)
fba_models[key] = {'cobra': cobra.io.read_sbml_model(source),
'doc': libsbml.readSBMLFromFile(source)}
elif value['sbo'] == 62:
print('ODE model')
# get the sbml file
modelRef = value["modelRef"]
mdoc = doc.getPlugin("comp")
emd = mdoc.getExternalModelDefinition(modelRef)
source = emd.getSource()
print(source)
else:
raise Exception("Modelling framework not supported, or not annotated on submodel: ", sbo)
# submodels handled by FBA
print(fba_models)
###########################
# Simulation
###########################
all_results = []
all_time = []
result = None
time = 0.0
while time <= tend:
if debug:
print("-" * 80)
print("Time: {}".format(time))
# --------------------------------------
# FBA
# --------------------------------------
# all fba submodels are simulated
for fba_key, fba_info in fba_models.iteritems():
cobra_model = fba_info['cobra']
sbml_model = fba_info['doc'].getModel()
# TODO: calculate once (not required in loop)
# which parameters are upper or lower bounds
from collections import defaultdict
ub_parameters = defaultdict(list)
lb_parameters = defaultdict(list)
for r in sbml_model.getListOfReactions():
mr = r.getPlugin("fbc")
rid = r.getId()
if mr.isSetUpperFluxBound():
ub_parameters[mr.getUpperFluxBound()].append(rid)
if mr.isSetLowerFluxBound():
lb_parameters[mr.getLowerFluxBound()].append(rid)
print(ub_parameters)
print(lb_parameters)
# search in global parameter replacements for replacements which replace the bounds
# of reactions
print("* set bounds *")
for p in model.getListOfParameters():
pid = p.getId()
mp = p.getPlugin("comp")
for rep_element in mp.getListOfReplacedElements():
# the submodel of the replacement belongs to the current model
if rep_element.getSubmodelRef() == fba_key:
# update upper and lower bounds
for rid in ub_parameters.get(pid, []):
print(rid, ': (upper) -> ', pid)
cobra_reaction = cobra_model.reactions.get_by_id(rid)
cobra_reaction.upper_bound = rr_comp[pid]
for rid in lb_parameters.get(pid, []):
print(rid, ': (lower) -> ', pid)
cobra_reaction = cobra_model.reactions.get_by_id(rid)
cobra_reaction.lower_bound = rr_comp[pid]
# [2] optimize
print("* optimize *")
# TODO: start with last solution (speed improvement)
cobra_model.optimize()
# [3] set fluxes in ODE part
print("* set fba fluxes in ode *")
# based on replacements the fluxes are written in the kinetic part
# set solution fluxes in parameters
for (rid, flux) in cobra_model.solution.x_dict.iteritems():
if rid in fba_rules:
rr_comp[fba_rules[rid]] = flux
print(rid, ':', fba_rules[rid], "=", flux)
else:
print(rid, "no boundary flux")
if debug:
print_flux_bounds(cobra_model)
print(cobra_model.solution.status)
print(cobra_model.solution.x_dict)
print("-" * 80)
# --------------------------------------
# ODE
# --------------------------------------
# With the updated fluxes from the FBA the kinetic part is
# calculated:
# simulate (1 step)
if step_size:
# constant step size
result = rr_comp.simulate(0, end=step_size, steps=1)
else:
# variable step size
result = rr_comp.simulate(0, steps=1, variableStep=True)
# store results
all_results.append(result[1])
# set the fba fluxes in the model)
# TODO: the fba fluxes are not set in the full kinetic result (shown as zero)
# these have to be set with the mapping between comp and flattened model
all_time.append(time)
# store simulation values & get time step
delta_time = result['time'][1]
time = time + delta_time
if debug:
print(result)
# create result matrix
df = pd.DataFrame(data=all_results, columns=result.colnames)
df.time = all_time
print(df)
return df